Floodplains provide multiple benefits to both resident and migratory fish species, including juvenile Chinook Salmon Oncorhynchus tshawytscha, but direct comparisons of survival during migration through a floodplain versus riverine routes are scarce. The Yolo Bypass is a broad floodplain of the Sacramento River that floods in about 30% of years in response to large, uncontrolled runoff events. We analyzed data from an acoustic telemetry study conducted in winter 2016 to estimate the proportion of tagged juvenile Chinook Salmon entrained from the Sacramento River into the Yolo Bypass and their spatial distribution within the Yolo Bypass. In addition, we compared survival and travel time of Chinook Salmon that migrated through the Yolo Bypass to those migrating via alternative non‐floodplain migration routes at varying stages of a flood event that activated the Yolo Bypass. We found that entrainment into the Yolo Bypass ranged from 1% to 80% among different release groups, with the highest entrainment coinciding with the peak of the March 2016 flooding event. Survival for Chinook Salmon migrating through the Yolo Bypass was similar to survival of those migrating through main‐stem migration routes. At the relatively high flows necessary to enable flooding of the Yolo Bypass, survival estimates varied little among release groups and migration routes. Furthermore, mean daily survival rates for Chinook Salmon migrating through the flooded Yolo Bypass were comparable to those of fish migrating through the other non‐floodplain routes. Median travel times remained relatively constant during various stages of flooding in the Yolo Bypass. This research should help managers to better understand the potential costs and benefits to floodplain restoration and routing of migrating Chinook Salmon into off‐channel habitat.